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Official Plugins
This page catalogues every plugin in MoleditPy's official collection — moleditpy-plugins, whose REGISTRY/plugins.json is the authoritative index read by both the in-browser Plugin Explorer and the Plugin Installer plugin. See Using Plugins for how to install any of these.
Six of the larger plugins have their own dedicated walkthrough page, linked from their entry below:
- ORCA Input Generator Pro — JP
- ORCA Result Analyzer — JP
- PySCF Calculator — JP
- Gaussian Input Generator Pro — JP
- CIF Viewer — JP
- PMEFF — JP
Unless noted otherwise, every plugin below supports Windows, macOS, Linux, and WSL, and Python >=3.9, <3.15, and is authored by HiroYokoyama.
| Plugin | Category | Menu location | Notes |
|---|---|---|---|
| Paste XYZ | File | File ▸ Paste XYZ... |
|
| Paste from ChemDraw | File | Edit ▸ Paste from ChemDraw |
Ctrl+Shift+V |
| OpenBabel Conversion Tool | File | fallback file importer + Export ▸ Export via OpenBabel...
|
|
| Cube File Viewer | File |
.cube/.cub file opener |
|
| Cube File Viewer Advanced | File |
.cube/.cub file opener |
PBR/SSAO rendering |
| Mapped Cube Viewer | File, Analysis | Plugins menu (legacy) | maps one cube onto another's isosurface |
| Orbital Comparator | Analysis, Visualization | Plugins menu (legacy) | up to 4 cubes at once |
| Encrypted Project | File |
.pmeenc opener + Export ▸ Export Encrypted (.pmeenc)...
|
AES-128 |
| Gaussian FCHK Loader | File, DFT |
.fchk/.fck/.fch opener (dispatcher) |
no menu entry |
| Gaussian Freq Analyzer | Analysis, DFT, File |
.fchk opener (via FCHK Loader) |
IR + normal modes |
| Gaussian MO Analyzer | Analysis, DFT, File, Visualization |
.fchk opener |
ships as a zip package |
| ORCA Freq Analyzer | Analysis, DFT, File |
.out/.log opener |
IR + normal modes |
| Blender Export | File, Visualization | Export ▸ Export to Blender Script... |
plain bpy script |
| POV-Ray Export | File, Visualization | Export ▸ Export to POV-Ray Scene... |
|
| xTB Optimizer | Optimization | 3D Edit ▸ xTB Optimizer… |
GFN2/GFN1-xTB via tblite |
| All-Trans Optimizer | Optimization | 3D Edit ▸ All-Trans Optimizer |
|
| Complex Molecule Untangler | Optimization | Plugins menu (legacy) | Monte Carlo declash |
| Conformational Search | Optimization | 3D Edit ▸ Conformational Search... |
ETKDG sampling |
| Step Optimizer | Optimization | 3D Edit ▸ Step Optimizer... |
live per-step animation |
| PMEFF | Optimization | selectable Optimize 3D method + Analysis/Settings/3D Edit
|
full periodic table FF — full page |
| Symmetry Analyzer | Analysis | 3D Edit ▸ Symmetrize... |
point group + symmetrization |
| Compound Info Report | Analysis | Analysis ▸ Compound Info Report... |
|
| MS Spectrum Simulation Neo | Analysis | Analysis menu (add_analysis_tool) |
|
| Molecule Comparator | Analysis, Visualization | Plugins menu (legacy) | multi-molecule RMSD/align |
| Atom Colorizer | Utility, Visualization | Plugins menu (legacy) | |
| Bond Colorizer | Utility, Visualization | Plugins menu (legacy) | |
| VDW Radii Overlay | Visualization | 3D style selector | merged VDW surface |
| Vector Viewer | Utility, Visualization | Plugins menu (legacy) | e.g. dipole moment |
| Advanced Rendering | Visualization |
Settings ▸ Advanced Graphics Settings + 3D styles |
lighting/SSAO/EDL/PBR |
| High Resolution Imager | Utility, Visualization | Export ▸ High Resolution Screenshot... |
|
| Dark Mode Theme | Visualization | none — applies automatically | autorun() |
| MOPAC Input Generator | DFT, Generator | Plugins menu (legacy) | |
| GAMESS Input Generator | DFT, Generator | Plugins menu (legacy) | |
| PySCF Input Generator | DFT, Generator, Utility | Plugins menu (legacy) | |
| Psi4 Input Generator | DFT, Generator | Plugins menu (legacy) | |
| NWChem Input Generator | DFT, Generator | Plugins menu (legacy) | |
| ORCA xyz2inp GUI | DFT, File, Generator | Plugins menu (legacy) | XYZ + templates |
| ORCA Input Generator Pro | DFT, Generator | Export ▸ ORCA Input... |
full page |
| ORCA Result Analyzer | Analysis, DFT, File |
.out opener + Extensions ▸ ORCA Result Analyzer
|
full page |
| Gaussian Input Generator Pro | File, Generator | Export ▸ Gaussian Input... |
full page |
| PySCF Calculator | DFT, Optimization, Visualization | Extensions ▸ PySCF Calculator... |
macOS/Linux/WSL only — full page |
| CIF Viewer | File |
View ▸ CIF Viewer Panel + .cif opener |
full page |
| Metadata Saver | Utility | Settings ▸ Metadata Saver... |
debug/trace metadata |
| Settings Saver | Utility | Settings ▸ Presets... |
|
| Structural Updater | Utility | Settings ▸ Structural Updater... |
|
| Dummy Atom Mode | Utility | 2D editor toolbar toggle |
* placeholder atoms |
| Plugin Installer | Utility | Plugin ▸ Plugin Installer... |
|
| Python Console | Utility | Plugins menu (legacy) |
mw/mol bound |
| XYZ Editor | Utility, Visualization | 3D Edit ▸ XYZ Editor... |
|
| Bond Editor | Utility | 3D Edit ▸ Bond Editor... |
|
| Charge Editor | Utility | 3D Edit ▸ Charge Editor... |
|
| PubChem Name Resolver | Utility | Plugins menu (legacy) | |
| PubChem Structure Identifier | Utility | Plugins menu (legacy) | |
| Chat with Molecule Neo (Gemini) | AI | Plugins menu (legacy) | |
| Chat with Molecule Neo (ChatGPT) | AI | Plugins menu (legacy) | |
| Chat with Molecule Neo (Local) | AI | Plugins menu (legacy) | local OpenAI-compatible server |
| MCP Server | AI | background service | Model Context Protocol |
| NICS Placer | Analysis, DFT |
3D Edit ▸ NICS Placer... / NICS Grid (2D, 3D)...
|
|
| Molibrary Browser | File | — | intranet chem database client |
| Animated XYZ Giffer | File, Visualization | Plugins menu (legacy) | multi-frame XYZ player + GIF recording |
| Rotation Giffer | File | Export ▸ Generate Rotation GIF... |
|
| Auto Rotator | Visualization | View ▸ Auto Rotator... |
live camera spin |
| 3D Molecule on 2D | File, Visualization | Settings ▸ 3D Molecule on 2D... |
depth cues on the 2D canvas |
| Reaction Sketcher | File, Utility, Visualization | 2D-canvas toolbar | reaction drawing tools |
| DECIMER Image Importer | File, Visualization | File ▸ Import from Image (DECIMER)... |
|
| Blender Export Pro | Visualization | Extensions ▸ Blender Export Pro... |
36 stylized presets |
| NMR Predictor (nmrshiftdb2) | Analysis | Analysis ▸ NMR Prediction (nmrshiftdb2) |
requires a JRE |
| VASP Input Generator | DFT, Generator | Export ▸ VASP Input (POSCAR/INCAR)... |
periodic |
| Quantum ESPRESSO Input Generator | DFT, Generator | Export ▸ Quantum ESPRESSO Input (pw.x)... |
periodic |
| CP2K Input Generator | DFT, Generator | Export ▸ CP2K Input (Quickstep)... |
periodic |
| Slab Builder | Utility | Structure ▸ Slab Builder... |
cuts (hkl) surface slabs, writes CIF |
| Job Manager | Utility |
Plugins ▸ Job Manager ▸ Job Monitor / Submit Job...
|
SSH cluster submission + .pmejbs opener |
| ORCA NICS Analyzer | Analysis, Visualization | Extensions ▸ ORCA NICS Analyzer... |
reads NICS out of an ORCA .out
|
| Strain Homodesmotic Reaction Generator | DFT | Analysis menu (add_analysis_tool) |
Pastes XYZ-format coordinates from the clipboard directly into a new 3D molecule. No dependencies. Menu: File ▸ Paste XYZ....
Parses ChemDraw's clipboard data format (MDLCT/MDLSK) so structures copied from ChemDraw paste straight into MoleditPy. Developed against ChemDraw 25.5. Dependency: RDKit. Menu: Edit ▸ Paste from ChemDraw (Ctrl+Shift+V).
Registers as a low-priority fallback file importer (register_file_opener(..., priority=-1)) for any format Open Babel understands, with multi-molecule import support, plus an Export ▸ Export via OpenBabel... action. Dependency: openbabel-wheel.
Visualizes Gaussian Cube files (orbitals, densities, and other volumetric data). Registers .cube/.cub as a file opener — no menu entry, just open or drag in a cube file. Dependencies: RDKit, PyVista, NumPy.
The same cube-visualization role as the basic viewer, but rendered with the same PBR/SSAO/other post-processing pipeline as Advanced Rendering. Also a .cube/.cub file opener. Dependencies: RDKit, PyVista, NumPy, PyQt6.
Maps a scalar property from one cube file (e.g. ESP) onto an isosurface generated from a second cube file (e.g. electron density) — the classic "ESP-mapped density surface" plot. Legacy run(mw) plugin, auto-registered in the Plugins menu. Dependencies: NumPy, PyVista, PyQt6, RDKit.
Loads and compares up to four .cube files side by side — each with its own colors, isovalue, opacity, and rendering style. Legacy run(mw) plugin (Plugins menu) that also conditionally registers a cube file opener. Dependencies: PyQt6, NumPy, PyVista.
Saves molecular/project data with AES-128 password protection into a .pmeenc file — registers both a .pmeenc file opener and an Export ▸ Export Encrypted (.pmeenc)... action. Dependency: cryptography.
A smart dispatcher, not a viewer in its own right: it registers .fchk/.fch/.fck as a file opener at high priority (100) and, based on the file's content, hands off to either the Gaussian Freq Analyzer or the Gaussian MO Analyzer. No menu entry. Dependency: PyQt6.
Analyzes vibrational frequencies from Gaussian FCHK files: an IR spectrum view, animated normal modes, and GIF export of the animation. Opens via the .fchk file association (through the FCHK Loader above) or the legacy Plugins-menu entry; its own direct menu action is disabled in favor of that dispatch. Dependencies: RDKit, PyQt6, NumPy, Pillow.
Visualizes molecular orbitals from Gaussian FCHK files by generating Cube files on the fly. Supports S, P, D, F, and spherical G shells — and, notably, rejects files whose basis functions it cannot render exactly rather than silently showing an incorrect surface. Ships as a multi-file zip package (gaussian_fchk_mo_analyzer/), unlike most bundled plugins' single .py file. Registers .fchk/.fch/.fck (priority 10) plus a drag-and-drop handler. Dependencies: RDKit, NumPy, PyVista, PyQt6.
The ORCA-output counterpart to Gaussian Freq Analyzer: IR spectrum, animated normal modes, GIF export, from an ORCA .out/.log file. Dependencies: RDKit, PyQt6, NumPy, Pillow.
Exports the current molecule as a plain Blender Python (bpy) script that recreates the 3D scene when run inside Blender — no Blender installation needed on the MoleditPy machine itself. Export ▸ Export to Blender Script.... Dependencies: RDKit, NumPy, PyQt6. (Distinct from the separate, more elaborate Blender Export Pro, §"AI-adjacent standalone plugins" below.)
Exports the current scene as a POV-Ray scene file for professional ray-traced rendering outside MoleditPy. Export ▸ Export to POV-Ray Scene.... Dependencies: RDKit, NumPy, PyQt6.
Plays multi-frame XYZ files (trajectories, IRC paths, optimization histories) frame by frame in the 3D viewer and records the animation to a GIF. The active successor to the retired Animated XYZ Player. Legacy run(mw) plugin (Plugins menu). Dependency: Pillow.
Geometry optimization using semiempirical xTB methods (GFN2-xTB, GFN1-xTB) via the tblite package, run on a background thread. 3D Edit ▸ xTB Optimizer…. Dependencies: tblite, ase. Windows note: install tblite from conda-forge (mamba install -c conda-forge tblite-python ase) — PyPI ships no Windows wheel, though the conda-forge channel does, so the plugin is not OS-restricted in the registry.
A purely geometric tool that straightens alkyl chains into their all-trans conformation, without a force-field relaxation. 3D Edit ▸ All-Trans Optimizer. Dependency: RDKit.
A Monte Carlo-based tool for resolving steric clashes in complex or roughly-drawn molecules — useful when a structure has been pasted or generated with atoms overlapping. Legacy run(mw) (Plugins menu). Dependency: RDKit.
Performs RDKit ETKDG-based conformational sampling and energy minimization to find low-energy conformers. 3D Edit ▸ Conformational Search.... Dependency: RDKit.
An interactive, step-by-step force-field optimizer with live 3D animation of each minimization step, so you can watch the structure relax in real time (and stop early if it looks wrong). 3D Edit ▸ Step Optimizer.... Dependency: RDKit.
A self-contained universal force field covering the entire periodic table (Z=1–118) — see the dedicated PMEFF plugin page for the full term-by-term breakdown, the Metal Geometry Override tool, and its two Analysis-menu diagnostics.
Analyzes molecular point-group symmetry and can symmetrize a structure to its ideal geometry. 3D Edit ▸ Symmetrize.... Dependencies: RDKit, PyQt6, pymatgen.
Generates a compound information report (properties, adducts, structure) — useful for documenting a synthesized compound. Analysis ▸ Compound Info Report.... Dependencies: RDKit, PyQt6.
Simulates the mass spectrum of the current molecule using RDKit descriptors, with Gaussian peak broadening and interactive zoom/pan. Registered via add_analysis_tool, so it lives in the Analysis menu. Dependencies: RDKit, NumPy, PyQt6.
Compares multiple molecules in 3D, computes RMSD, and aligns them — also adds right-click "Export Coordinates as MOL/XYZ" actions. Legacy run(mw) (Plugins menu). Dependencies: RDKit, PyQt6.
Select atoms in the 3D viewer and apply a color, persisted with the project. Legacy run(mw) (Plugins menu). Dependencies: NumPy, PyVista, PyQt6.
The bond equivalent of Atom Colorizer — select bonds by index or atom pair in the 3D viewer and color them. Legacy run(mw) (Plugins menu). Dependencies: NumPy, PyVista, PyQt6.
Visualizes Van der Waals radii as a single merged surface overlay (rather than per-atom spheres) using PyVista. Registered as a selectable 3D rendering style, with no separate menu entry. Dependencies: PyVista, NumPy, PyQt6.
Visualizes vectors attached to the molecule — e.g. the dipole moment — in 3D, with PNG export of the view. Legacy run(mw) (Plugins menu). Dependencies: NumPy, PyQt6, PyVista.
Fine-grained control over scene lighting, shadows, post-processing effects (SSAO, Depth Peeling, EDL), and atom/bond rendering (PBR, Silhouette). Registers several selectable 3D styles plus Settings ▸ Advanced Graphics Settings. Dependencies: PyVista, PyQt6, NumPy.
Captures a high-resolution screenshot of the 3D view at a custom resolution, independent of your monitor's size. Export ▸ High Resolution Screenshot.... Dependencies: PyVista, PyQt6.
Automatically applies a dark-mode stylesheet to the whole application on load — an autorun() plugin with no menu entry at all; just install it and restart. Dependency: PyQt6.
Five plugins share the same design: a legacy run(mw) dialog (auto-registered in the Plugins menu, no initialize()), a common "no molecule loaded" warning guard, and a focus on writing plain input text for one specific QM package. Dependencies: RDKit, PyQt6 for each.
| Plugin | Target package |
|---|---|
| MOPAC Input Generator | MOPAC semi-empirical calculations |
| GAMESS Input Generator | GAMESS (US) |
| PySCF Input Generator | Generates a standalone PySCF Python script (rather than driving a calculation directly — see PySCF Calculator for that) |
| Psi4 Input Generator | Psi4 |
| NWChem Input Generator | NWChem |
A simpler, older sibling of ORCA Input Generator Pro: generates ORCA input files from XYZ data using templates. Ships from its own repository (orca_xyz2inp) rather than moleditpy-plugins itself, but its download is listed as a bundled-style plain .py file. Legacy run(mw) (Plugins menu). Dependencies: RDKit, PyQt6. Compatible back to MoleditPy 3.0.0.
Four plugins, each in its own repository, cover periodic DFT. The three input generators share the same design: three structure sources — the molecule currently open in MoleditPy (wrapped in an orthorhombic vacuum box), a .cif read from disk (asymmetric unit expanded with the file's own symmetry operations), or the structure already loaded in the CIF Viewer panel — plus independent a/b/c supercell repeats, per-axis vacuum padding for slab setups, and a k-mesh that can be derived from a target reciprocal-space spacing. Dependencies: NumPy, PyVista, RDKit for each.
Writes POSCAR/INCAR/KPOINTS. Task presets for single point, ionic relaxation, ionic + cell relaxation, DOS, non-SCF band structure and NVT MD; INCAR control over functional (PBE/PBEsol/RPBE/LDA), ENCUT, EDIFF/EDIFFG, smearing, spin polarization with an initial MAGMOM guess, dispersion (D2/D3/D3-BJ/TS) and the usual PREC/ALGO/LREAL/NELM/NCORE knobs, plus a free-text block. Atoms selected in MoleditPy can be frozen via selective dynamics. POTCAR files are licensed VASP data and are never generated — instead you get a ready-to-run cat command over the recommended PAW set in POSCAR element order. A warning strip flags the classic mistakes (dense k-mesh on an isolated molecule, k-points across a slab's vacuum, too little vacuum). Export ▸ VASP Input (POSCAR/INCAR)....
Writes pw.x inputs for every run type (scf, nscf, bands, relax, vc-relax, md, vc-md), with &IONS/&CELL emitted only when the run type needs them. ecutwfc with an automatic ecutrho = 8 × ecutwfc, occupations and smearing, nspin = 2 with per-type starting_magnetization, input_dft overrides, vdw_corr (D2/D3/XDM/TS), and full &ELECTRONS control. ATOMIC_SPECIES carries IUPAC masses and UPF filenames resolved by scanning your pseudopotential folder, with an editable {El}/{el}/{EL} filename pattern as the fallback; charge and open-shell state are read from the molecule. Export ▸ Quantum ESPRESSO Input (pw.x)....
Writes Quickstep inputs for ENERGY_FORCE, GEO_OPT, CELL_OPT and MD. MOLOPT basis sets with matching GTH potentials per &KIND (the potential follows the functional — GTH-PBE, GTH-BLYP, GTH-PADE), charge and multiplicity with UKS forced when needed, &MGRID cutoffs, &QS EPS_DEFAULT, PBE/BLYP/BP/PADE/PBE0/B3LYP and DFT-D2/D3/D3(BJ) dispersion. Two SCF strategies: &OT with &OUTER_SCF for insulators and molecules, or diagonalization with Fermi-Dirac &SMEAR, ADDED_MOS and Broyden mixing for metals, since OT cannot handle fractional occupations. Export ▸ CP2K Input (Quickstep)....
Cuts a surface slab out of a bulk crystal and writes it back as a P1 CIF, which any of the three generators above reads straight back in. The surface basis is built from the (hkl) Miller indices so a/b lie in the surface plane and c stacks it; hexagonal Miller-Bravais (hkil) indices are accepted and folded to (hkl). Layer count, vacuum thickness split evenly across both faces, a termination shift that slides a constant-thickness cut window through the bulk cell (so the atom count never changes as you scan terminations), and a/b/c supercell repeats of the finished slab. Bulk comes from a .cif on disk or from the CIF Viewer panel. Structure ▸ Slab Builder....
Saves debug/trace metadata (timestamp, file path, username, OS info, …) into the .pmeprj project file, for debugging and tracing. The plugin's own description warns: do not share project files containing this data with anonymous users. Settings ▸ Metadata Saver.... No dependencies.
Save, load, and manage settings presets in one unified dialog. Settings ▸ Presets.... Dependency: PyQt6.
Applies 2D structural edits to the existing 3D conformation without a full re-embedding — useful for small edits (adding a substituent, say) where you don't want to lose the rest of the optimized geometry. Settings ▸ Structural Updater.... Dependencies: RDKit, PyQt6.
Adds a dummy-atom (*) placement mode to the 2D editor via a toolbar toggle, rather than a menu action. Dependencies: RDKit, PyQt6.
Checks for updates against the official registry, installs new plugins, and allows manual reinstallation — all from inside MoleditPy. Plugin ▸ Plugin Installer.... See Using Plugins §7 for how it fits into the overall install flow. Dependency: PyQt6.
An interactive Python interpreter embedded in the application, with mw (MainWindow) and mol (current molecule) bound in its namespace for runtime scripting. Legacy run(mw) (Plugins menu). Has no sandboxing — it can execute arbitrary code you type. Dependencies: RDKit, PyQt6.
A table-based editor for atom coordinates and element symbols, supporting ghost atoms and adding/deleting atoms directly in the table. 3D Edit ▸ XYZ Editor.... Dependencies: RDKit, PyQt6.
A table-based bond editor: add/delete bonds, change bond order, and set bond length by dragging one side of the bond — plus a 3D pick mode to select an existing bond by clicking it, or create a new one by clicking two atoms in sequence. 3D Edit ▸ Bond Editor.... Dependencies: RDKit, PyQt6, PyVista, NumPy.
A table-based editor for per-atom formal charge and radical electron count. Click atoms in the 3D view to select them, and read off the resulting total charge and spin multiplicity — handy for setting up DFT input correctly. 3D Edit ▸ Charge Editor.... Dependencies: RDKit, PyQt6, PyVista, NumPy.
Resolves chemical names and identifiers to structures via the PubChem PUG REST API. Legacy run(mw) (Plugins menu). Dependencies: requests, RDKit.
Resolves a chemical name and fetches its molecular properties (Name, Formula, Weight) from PubChem. Legacy run(mw) (Plugins menu). Dependencies: RDKit, PyQt6.
Three variants of the same tool — chat with an LLM about the currently loaded molecule, with SMILES context automatically injected into the conversation. All three are legacy run(mw) plugins (Plugins menu) with no separate menu action, and share dependencies RDKit, PyQt6, markdown, matplotlib.
| Variant | Backend | Extra dependency |
|---|---|---|
| Chat with Molecule Neo (Gemini) | Google Gemini | google-genai |
| Chat with Molecule Neo (ChatGPT) | OpenAI ChatGPT | openai |
| Chat with Molecule Neo (Local) | Any local OpenAI-compatible server |
openai (client library only — no cloud calls to OpenAI itself; note the InChIKey used for the PubChem lookup step is still sent to PubChem, not to your local model) |
Exposes MoleditPy over the Model Context Protocol so AI assistants (Claude Desktop and others) can drive the application directly — file/plugin discovery, molecule inspection, and editing tools. Ships from its own repository (moleditpy-mcp_server) as a background service rather than a dialog-based plugin. No Python dependencies beyond the host app itself.
Detects rings in the current 3D structure (aromatic and non-aromatic) and places Bq ghost atoms at NICS(0)/NICS(1)± probe positions — NICS(1)± uses an SVD best-fit ring plane, with an adjustable probe height for variants like NICS(0.5)/NICS(2). Compatible with ORCA Input Generator Pro via the custom_symbol property, so probes carry through into the generated .inp. A companion Grid mode places a rectangular plane/box of probes for 2D/3D scans. 3D Edit ▸ NICS Placer... and 3D Edit ▸ NICS Grid (2D, 3D).... Dependencies: RDKit, PyQt6.
The read side of a NICS study: place ghost probes (with NICS Placer or otherwise), run the ORCA NMR job, then open the .out here. What you get depends on how the probes were laid out — a Probes table of NICS(0)/NICS(1), NICS_zz, distance from the ring plane and aromatic/antiaromatic character for one or a few probes; a 1D Scan profile with the extremum marked for a line of probes; a 2D Map of filled NICS contours with the molecule projected on top for a plane of probes; and 3D ICSS ± isosurfaces drawn in MoleditPy's own 3D viewer for a box of probes. Everything exports — probe/scan/grid CSV, plot images (PNG/PDF/SVG), Gaussian .cube files and a text summary — per tab or all at once. matplotlib and PyVista are optional at runtime: without them the tabs that need them explain what is missing and the rest keeps working. Ships from its own repository (moleditpy_orca_nics_analyzer). Extensions ▸ ORCA NICS Analyzer.... Dependencies: PyQt6, NumPy, matplotlib, PyVista.
Connects MoleditPy to a local Molibrary server — a standalone intranet chemistry structure-and-protocol database — for searching and importing structures. Ships from the chem_db_web repository rather than a moleditpy_*-named one. Dependencies: RDKit, PyQt6.
Exports a rotating GIF by orbiting the camera around either global (X/Y/Z) or local view (Roll/Pitch/Yaw) axes, with an inverse-rotation toggle, configurable total angle (10°–3600°), frame count, and FPS, transparent-background export, and SSAA plus adaptive color quantization to avoid GIF color banding. Export ▸ Generate Rotation GIF.... Dependencies: PyVista, PyQt6; Pillow is optional but strongly recommended (needed for transparent export and the quantization pipeline).
Continuously spins the 3D viewer by orbiting the camera around a chosen axis — Global X/Y/Z or view-relative Roll/Elevation/Azimuth — at an adjustable, sign-reversible °/s speed, for live presentation (a non-recording companion to Rotation Giffer). View ▸ Auto Rotator.... Dependencies: PyVista, PyQt6, NumPy.
Brings 3D depth cues, rotation, and 3D-aware export into the 2D editor: distance-based depth-fade coloring of 2D atoms/bonds, dragging an atom or bond on the 2D canvas to rotate the whole molecule about its center of gravity, a "Clean Up 3D" smart-sync action (fast realignment if only positions changed, full re-embed if the topology changed), and a .mol exporter that preserves the true Z-coordinates instead of flattening them. Settings ▸ 3D Molecule on 2D.... Dependencies: RDKit, PyQt6, NumPy.
Adds a dedicated 2D reaction-drawing toolset directly on the main canvas: reaction arrows (forward, equilibrium, resonance, retrosynthetic, dashed, no-reaction), curved single/double electron-pushing arrows, text/plus/minus annotations, brackets (square/round/curly) and circles/ellipses, grouping (Ctrl+G/Ctrl+U) and alignment/distribution tools, a typography toolbar with chemistry auto-subscripting (typing H2O renders as H₂O), full undo/redo integration, a Shift+Right-Click context menu, and 15° angle snapping (hold Alt to bypass). Dependencies: RDKit, PyQt6.
Predicts a SMILES structure from a PNG/JPG/JPEG chemical-structure drawing using the DECIMER deep-learning model, running inference on a background thread (typically 10–30 seconds) so the UI stays responsive; drag-and-dropping an image file onto the main window also triggers prediction. File ▸ Import from Image (DECIMER).... Dependencies: DECIMER (pulls in TensorFlow) and Pillow — on Windows, install tensorflow-cpu before DECIMER, and the plugin runs TensorFlow inference in an isolated subprocess to avoid a DLL conflict with PyQt6/PyVista.
A stylized/deformed Blender exporter with a live 3D preview: a tabbed dialog (Presets, Atoms, Bonds, Deformation, Material, Scene, Export) with 36 bundled presets (Classic Ball-and-Stick, CPK, Cute Cartoon, Glass Sculpture, Claymation, Neon Glow, Chrome Showroom, and more), custom JSON preset save/load, ring-panel and ring-outline rendering (filled hexagon plates or perimeter tubes with per-ring styling), and one-click bpy script generation whose preview mirrors what the generated script will produce. Extensions ▸ Blender Export Pro..., and also registers a "Blender Export Pro (Preview)" 3D style. No extra Python dependencies — Blender itself is not required on the MoleditPy machine. Distinct from the simpler, bundled Blender Export plugin above.
Predicts 1H and 13C NMR shifts using the nmrshiftdb2 prediction engine, shown as an interactive stick spectrum where hovering a peak or a table row highlights the corresponding atom in the 3D view. Analysis ▸ NMR Prediction (nmrshiftdb2). Dependencies: RDKit, PyVista, NumPy, matplotlib, PyQt6 — plus a Java Runtime Environment (JRE 8+) on PATH, since the prediction engine itself is the nmrshiftdb2 Java library (bundled .jar files), not a Python package. This is the only official plugin with a non-Python runtime requirement.
Detects bonding environments typical of strained or constrained molecules (ketones, aldehydes, primary/secondary/tertiary amines, extended alkanes) and builds a draft homodesmotic/isodesmic reaction balance via a MILP solve (falls back to simple elemental balancing if SciPy is unavailable), with an interactive colored reaction-equation display, the ability to load a reference species straight back into MoleditPy, and CSV/HTML/TXT export. Registered via add_analysis_tool rather than a raw menu path, so it appears in the Analysis menu as "Homodesmotic Reaction". Dependencies: NumPy, SciPy. Compatible back to MoleditPy 3.0.0 (an older floor than most other plugins here, which require 4.0.0).
Submits calculations to remote HPC clusters over SSH, tracks their queue status, and fetches results back into MoleditPy — with ready-made command lines for ORCA, Gaussian, CP2K, GAMESS, MOPAC, NWChem, Psi4, PySCF, Quantum ESPRESSO, VASP and xTB. It also runs jobs on the local machine with no SSH at all, chains jobs using each scheduler's own dependency flag, and can hold a job until a chosen time. Work that is already on the cluster needs no upload: point a job at a directory prepared there and give it a command, with an input file named in that directory or none at all — the directory is checked rather than created, and everything the wrapper writes into it carries the job id, so several jobs can share one prepared directory. A job can also reuse a file from another job on the same host — a [prevfile:.ext] tag written into the input (e.g. an ORCA * xyzfile or a Gaussian %oldchk) is resolved to the real filename and copied over on the host itself when the job is submitted; picking a job that has not finished yet chains the new one to start only once it succeeds. ORCA Input Generator Pro and Gaussian Input Generator Pro both grow a checkbox that writes this tag, plus a Submit to Cluster... button, when this plugin is installed. Drop several files on the monitor to submit each as its own job (batch), or hold Shift to combine them into one job instead; the job table sorts by clicking a column header and filters as you type. Job lists export to CSV or .pmejbs and reopen by drag and drop (.pmejbs is registered as a file opener). Ships from its own repository (moleditpy_job_manager). Plugins ▸ Job Manager ▸ Job Monitor and ▸ Submit Job.... No extra dependencies.
The following plugins are frozen in moleditpy-plugins/plugins/_old/ (registry entries with "visible": false, kept only so old download links don't break) and are not part of the active catalogue: Animated XYZ Player, Chat with Molecule (pre-Neo), Gaussian Input Generator, Gaussian Input Generator Neo, Hello World, Hello World Folder Plugin, MS Spectrum Simulation (pre-Neo), ORCA Input Generator, ORCA Input Generator Neo, and Version Checker.
- Using Plugins — installing, managing, and trusting plugins
- Plugin: ORCA Input Generator Pro
- Plugin: ORCA Result Analyzer
- Plugin: PySCF Calculator
- Plugin: Gaussian Input Generator Pro
- Plugin: CIF Viewer
- Plugin: PMEFF
- Official Plugins (JP)
This catalogue was written on 2026-08-05. For each plugin's current version, see REGISTRY/plugins.json or the Plugin Explorer.